From: Sebastian Stolzenberg (s.stolzenberg_at_gmail.com)
Date: Fri Apr 10 2009 - 18:22:15 CDT

Dear All,

I had started an equilibration run *without* CMAP corrections, having used

"topology top_all27_prot_lipid.inp":
*>>>>>> Combined CHARMM All-Hydrogen Topology File for <<<<<<<<<
*>>>>>>>>> CHARMM22 Proteins and CHARMM27 Lipids <<<<<<<<<<
...

I need to switch this equilibration run to CMAP (the equilibrations I
did so far mainly dealt with protein-lipid interactions):

"topology top_all27_prot_lipid_noHH.rtf":
*>CHARMM22 All-Hydrogen Parameter File for Proteins and Lipids <<
*>>>>> Includes phi, psi cross term map (CMAP) correction <<<<<<<
...

The initial psf *without* CMAP had entries:
 PSF
...
 REMARKS topology ./toppar/top_all27_prot_lipid.inp
 REMARKS topology ./toppar/top_all27_prot_lipid_noHH.inp
...

my new psf *with* CMAP now has entries:
 PSF CMAP
...
 REMARKS topology ./toppar/top_all27_prot_lipid_noHH.rtf
 REMARKS topology ./toppar/top_all27_prot_lipid.inp
 REMARKS topology ./toppar/top_all27_prot_lipid_noHH.inp
...
(cross-terms)

Within the CMAP psf, why are there the two other topology entries? (I
double-checked and made a blank restart of VMD, only *one* topology file
was read in.)
What are the overriding rules for topology files, if any?

Thank you,
Best,
Sebastian